SRA has done away with SRX experiment directories on FTP site: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/.... might be temporarily down

Question

[chrisclarkson100]

I have been trying all day to access different SRA files on the GEO database but keep being met with '404' kind of error- stating that the site is down. I have tried on two separate computers and get the same result... taking the following path as an example:

ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX232/SRX2327412

The above path only exists as far as ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/

i.e. there is no 'SRX' directory....

Is it normal for all SRA files on the GEO database to be (temporarily?) inaccessible? If so how long does this tend to last?

[Ram]

SRX is not a valid identifier prefix as far as I can see. The X is most probably a stand-in for eXperiment until an actual P or R or whatever gets assigned, I think.

Answer 1

[chrisclarkson100]

After contacting SRA. It appears that they have done away with the 'SRX' experiment directory: "The size of the SRA prevents the use of an FTP tree centered around experiments and had to be taken down. If you really need to use the old method of an FTP tree then look at the Runs organized by a study."

[GenoMax]

Edit the title of this post and put something along the lines of SRA has done away with SRX experiment directories on FTP site. That would make this thread useful to someone searching for a similar issue in future.

Answer 2

[GenoMax]

This dataset is NOT public at this time and that may be the reason.

[chrisclarkson100]

Thank you for this information but when I try to access the following ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX134/SRX1342333 (also not available). I then search it on the SRA database: SRX1342333 like you did and it is available.... However I just can't seem to access the sra files....

[GenoMax]

Mysteries of SRA :) Email SRA support and ask them. ENA does not seem to have that data either.

Answer 3

[EagleEye]

You can alternately download directly from the ENA deposit (PRJNA299026, GSE74112),

https://www.ebi.ac.uk/ena/data/view/SRP064924

1) Download the text file generated from ENA/SRA

2) Use the links (column: FASTQ files (FTP)) from the text file to download compressed fastq file (*fastq.gz) (I personally loop over the column to download all files parallel)

The above procedure you can do when the data is public but not accessible directly via GEO repository. If the data is not public you will not have access link in ENA/SRA.